1
|
Deng A, Li J, Yao Z, Afriyie G, Chen Z, Guo Y, Luo J, Wang Z. SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata. Front Genet 2021; 12:741243. [PMID: 34721529 PMCID: PMC8552913 DOI: 10.3389/fgene.2021.741243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/24/2021] [Indexed: 11/24/2022] Open
Abstract
Coelomactra antiquata is an important aquatic economic shellfish with high medicinal value. However, because C. antiquata has no reference genome, a lot of molecular biology research cannot be carried out, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. antiquata. In the present study, we conducted the first full-length transcriptome analysis of C. antiquata by using PacBio single-molecule real-time (SMRT) sequencing technology. The results identified a total of 39,209 unigenes with an average length of 2,732 bp, 23,338 CDSs, 251 AS events, 9,881 lncRNAs, 20,106 SSRs, and 2,316 TFs. Subsequently, 59.22% (23,220) of the unigenes were successfully annotated, of which 23,164, 18,711, 15,840, 13,534, and 13,474 unigenes could be annotated using NR, Swiss-prot, KOG, GO, and KEGG databases, respectively. This study lays the foundation for the follow-up research of molecular biology and provides a reference for studying the more medicinal value of C. antiquata.
Collapse
Affiliation(s)
- Aiping Deng
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jinpeng Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zebin Yao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Gyamfua Afriyie
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Ziyang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yusong Guo
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jie Luo
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongduo Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| |
Collapse
|
2
|
Fernández-Pérez J, Nantón A, Ruiz-Ruano FJ, Camacho JPM, Méndez J. First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order. PLoS One 2017; 12:e0184464. [PMID: 28886105 PMCID: PMC5590976 DOI: 10.1371/journal.pone.0184464] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Four species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management. PRINCIPAL FINDINGS The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic. CONCLUSIONS Sequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource.
Collapse
Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | | | - Juan Pedro M. Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| |
Collapse
|
3
|
Shen X, Song J, Meng X, Tian M, Yan B, Cheng H, Cai Y, Zhao J. The first representative of Coelomactra antiquata mitochondrial genome from Liaoning (China) and phylogenetic consideration. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:525-527. [PMID: 33473543 PMCID: PMC7800962 DOI: 10.1080/23802359.2016.1197064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Coelomactra antiquata is a famous delicacy and a promising new candidate for aquaculture, which belongs to the family Mactridae (Mollusca: Veneroida). The complete mitochondrial genome of C. antiquata (Liao Ning province, in China, LN) was finished, which is the first representative from this province. The results showed that the total length of LN-mtDNA sequence is 16,797 bp and the content of A + T is 65.01%. It encodes 35 genes, including 12 protein-coding genes, 21 transfer RNA genes and two ribosomal RNA genes. All coding genes are encoded on the heavy strand. Compared with the typical gene content of animal mitochondrial genomes, atp8 and trnSer(UCN) genes are missing in the mitochondrial genome. The complete mitochondrial genome contains 26 non-coding regions (1598 bp), one major non-coding region consists of 1046 bp in which 4.9 tandem repeat sequences (99bp per sequence) was observed. The phylogenetic tree showed that Liaoning population was clustered into one clade with Shandong (Rizhao, Jiaonan and Jimo) and Guangxi (Beihai) populations, meanwhile all of them are far from the Fujian populations (Pingtan, Zhangzhou and Changle). So, Liaoning, Shandong and Guangxi populations have a close relationship. Actually, Fujian is located between Liaoning, Shandong and Guangxi. So, the result challenges the previously assumed relevance between geographic distance and genetic distance. The genetic distance of Liaoning C. antiquata and Fujian (Changle, Zhangzhou and Pingtan) C. antiquata (0.176–0.177) is greater than the genetic distance between Mytilus galloprovincialis and Mytilus trossulus (0.160). The genetic difference of Liaoning population and Fujian populations has reached species level.
Collapse
Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China.,College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Jun Song
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Xueping Meng
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China
| | - Binlun Yan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China.,College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Hanliang Cheng
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Yuling Cai
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Jun Zhao
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| |
Collapse
|
4
|
Hwang JY, Lee CK, Kim H, Nam BH, An CM, Park JY, Park KH, Huh CS, Kim EB. Comparative genomic analysis of mitochondrial protein-coding genes in Veneroida clams: Analysis of superfamily-specific genomic and evolutionary features. Mar Genomics 2015; 24 Pt 3:329-34. [PMID: 26343338 DOI: 10.1016/j.margen.2015.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 12/30/2022]
Abstract
Veneroida is the largest order of bivalves, and these clams are commercially important in Asian countries. Although numerous studies have focused on the genomic characters of individual species or genera in Veneroida, superfamily-specific genomic characters have not been determined. In this study, we performed a comparative genomic analysis of 12 mitochondrial protein coding genes (PCGs) from 25 clams in six Veneroida superfamilies to determine genomic and evolutionary features of each superfamily. Length and distribution of nucleotides encoding the PCGs were too variable to define superfamily-specific genomic characters. Phylogenetic analysis revealed that PCGs are suitable for classification of species in three superfamilies: Cardioidea, Mactroidea, and Veneroidea. However, one species classified in Tellinoidea, Sinonovacula constricta, was evolutionarily closer to Solenoidea clams than Tellinoidea clams. dN/dS analysis showed that positively selected sites in NADH dehydrogenase subunit, nd4 and subunit of ATP synthase, atp6 were present in Mactroidea. Differences in selected sites in the nd4 and atp6 could be caused by superfamily-level differences in sodium transport or ATP synthesis functions, respectively. These differences in selected sites in NADH may have conferred these animals, which have low motility and do not generally move, with increased flexibility to maintain homeostasis in the face of osmotic pressure. Our study provides insight into evolutionary traits as well as facilitates identification of veneroids.
Collapse
Affiliation(s)
- Jae Yeon Hwang
- Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921 Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Kangwon-do 232-916, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921 Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Kangwon-do 232-916, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Cheul Min An
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Kyu-Hyun Park
- Department of Animal Life System, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chul-Sung Huh
- Graduate School of International Agricultural Technology/GBST, Seoul National University, Pyeongchang 232-916, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
| |
Collapse
|
5
|
Shen X, Meng X, Tian M, Yan B, Cheng H, Lu W, Chai Y. The first mitochondrial genome of Coelomactra antiquata (Mollusca: Veneroida: Mactridae) from Guangxi (China) and potential molecular markers. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3642-3. [PMID: 26329456 DOI: 10.3109/19401736.2015.1079835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Coelomactra antiquata (Guangxi, in China, GX) was determined. It is 16 801 bp in length and is the first representative from this province. The mitochondrial genome encodes 35 genes, including 12 PCGs, two ribosomal RNA, and 21 transfer RNA genes. Atp8 and trnSer(UCN) genes are missing, compared with the typical gene content of animal mitochondrial genomes. Three (cob, nad1, nad4, and nad6) of the 12 PCGs in the mitochondrial genome initiate with the ATA, while other PCGs start with ATG. Two PCGs (atp6 and nad4L) end with incomplete stop codons (T-), and the remaining ones have complete stop codons (TAA or TAG). The largest non-coding region of the C. antiquata (GX) contains one section of tandem repeats (5 × 99 bp). Among all PCGs and rRNAs, the nad5 gene contains the maximum polymorphic sites (430), followed by nad4 (261) and cox2 (240). Two ribosomal RNA genes (srRNA and lrRNA) and cox1 are most conservative. The proportions of polymorphic sites in six genes (nad4, nad2, nad6, nad5, cox2, and nad3) are more than 20% (ranging from 20.25% to 25.21%). These high variable genes can be used as molecular markers in the population genetic analysis of the species.
Collapse
Affiliation(s)
- Xin Shen
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China .,b Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology , Lianyungang , China , and.,c Jiangsu Institute of Marine Resources , Lianyungang , China
| | - Xueping Meng
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
| | - Mei Tian
- b Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology , Lianyungang , China , and
| | - Binlun Yan
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China .,b Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology , Lianyungang , China , and
| | - Hanliang Cheng
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
| | - Wei Lu
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
| | - Yuling Chai
- a Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
| |
Collapse
|
6
|
Gan HM, Gan HY, Tan MH, Penny SS, Willan RC, Austin CM. The complete mitogenome of the giant clam Tridacna squamosa (Heterodonta: Bivalvia: Tridacnidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3220-1. [PMID: 25648928 DOI: 10.3109/19401736.2015.1007355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the commercially and ecologically important and internationally vulnerable giant clam Tridacna squamosa was recovered by genome skimming using the MiSeq platform. The T. squamosa mitogenome has 20,930 base pairs (62.35% A+T content) and is made up of 12 protein-coding genes, 2 ribosomal subunit genes, 24 transfer RNAs, and a 2594 bp non-coding AT-rich region. The mitogenome has a relatively large insertion in the atp6 gene. This is the first mitogenome to be sequenced from the genus Tridacna, and the family Tridacnidae and represents a new gene order.
Collapse
Affiliation(s)
- Han Ming Gan
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Petaling Jaya , Selangor , Malaysia .,b Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan , Petaling Jaya , Selangor , Malaysia
| | - Huan You Gan
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Petaling Jaya , Selangor , Malaysia .,b Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan , Petaling Jaya , Selangor , Malaysia
| | - Mun Hua Tan
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Petaling Jaya , Selangor , Malaysia .,b Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan , Petaling Jaya , Selangor , Malaysia
| | - Shane S Penny
- c Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin , Australia , and
| | - Richard C Willan
- d Museum and Art Gallery of the Northern Territory , Darwin , Australia
| | - Christopher M Austin
- a School of Science, Monash University Malaysia, Jalan Lagoon Selatan , Petaling Jaya , Selangor , Malaysia .,b Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan , Petaling Jaya , Selangor , Malaysia .,c Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin , Australia , and.,d Museum and Art Gallery of the Northern Territory , Darwin , Australia
| |
Collapse
|
7
|
Saunier A, Garcia P, Becquet V, Marsaud N, Escudié F, Pante E. Mitochondrial genomes of the Baltic clam Macoma balthica (Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities. BMC Evol Biol 2014; 14:259. [PMID: 25527898 PMCID: PMC4302422 DOI: 10.1186/s12862-014-0259-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Allopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous F ST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform. RESULTS The mitogenome has an approximate length of 16,806 bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNA (Met) and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations. CONCLUSIONS Six nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH dehydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica.
Collapse
Affiliation(s)
- Alice Saunier
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Pascale Garcia
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Vanessa Becquet
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Nathalie Marsaud
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, 31326, France.
| | - Frédéric Escudié
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, 31326, France.
| | - Eric Pante
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| |
Collapse
|
8
|
Sun S, Kong L, Yu H, Li Q. The complete mitochondrial DNA of Tegillarca granosa and comparative mitogenomic analyses of three Arcidae species. Gene 2014; 557:61-70. [PMID: 25499696 DOI: 10.1016/j.gene.2014.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 12/05/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
Abstract
To better understand the characteristics and the evolutionary dynamics of mt genomes in Arcidae, the complete mitochondrial genome of Tegillarca granosa was firstly determined and compared with other two Arcidae species (Scapharca broughtonii and Scapharca kagoshimensis). The complete mitochondrial genome of T. granosa was 31,589 bp in length, including 12 protein-coding genes, 2 rRNA genes and 23 tRNA genes, and a major non-coding region. Three tandem repeat fragments were identified in the major non-coding region and the tandem repeat motifs of these fragments can be folded into stem-loop structures. The mitochondrial genome of the three species has several common features such as the AT content, the arrangement of the protein-coding genes, the codon usage of the protein-coding genes and AT/GC skew. However, a high level of variability is presented in the size of the genome, the number of tRNA genes and the length of non-coding sequences in the three mitogenomes. According to the phylogenetic analyses, these mitogenome-level characters are correlated with their phylogenetic relationships. It is the absence of the duplicated tRNAs and large non-coding sequences that are responsible for the length divergence of mitogenomes between T. granosa and other two Arcidae species. The phylogenetic analyses were conducted based on 12 partitioned protein genes, which support the relationship at the family level: (((Pectinidae+Ostreidae)+Mytilidae)+Arcidae).
Collapse
Affiliation(s)
- Shao'e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| |
Collapse
|
9
|
Gan HM, Tan MH, Thai BT, Austin CM. The complete mitogenome of the marine bivalve Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:335-6. [PMID: 24617474 DOI: 10.3109/19401736.2014.892104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the commercially important snout otter clam Lutraria rhynchaena was obtained from low-coverage shotgun sequencing data on the MiSeq platform. The L. rhynchaena mitogenome has 16,927 base pairs (69% A + T content) and made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 953 bp non-coding AT-rich region. This is the first mitogenome to be sequenced from the genus Lutraria, and the seventh to be reported for the family Mactridae.
Collapse
Affiliation(s)
- Han Ming Gan
- a School of Science, Monash University Malaysia , Selangor , Malaysia and
| | - Mun Hua Tan
- a School of Science, Monash University Malaysia , Selangor , Malaysia and
| | - Binh Thanh Thai
- b Fisheries College , Dinh Bang, Tu Son , Bac Ninh , Viet Nam
| | | |
Collapse
|
10
|
Plazzi F, Ribani A, Passamonti M. The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with conchifera. BMC Genomics 2013; 14:409. [PMID: 23777315 PMCID: PMC3704766 DOI: 10.1186/1471-2164-14-409] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 06/11/2013] [Indexed: 11/17/2022] Open
Abstract
Background Bivalve mitochondrial genomes exhibit a wide array of uncommon features, like extensive gene rearrangements, large sizes, and unusual ways of inheritance. Species pertaining to the order Solemyida (subclass Opponobranchia) show many peculiar evolutionary adaptations, f.i. extensive symbiosis with chemoautotrophic bacteria. Despite Opponobranchia are central in bivalve phylogeny, being considered the sister group of all Autobranchia, a complete mitochondrial genome has not been sequenced yet. Results In this paper, we characterized the complete mitochondrial genome of the Atlantic awning clam Solemya velum: A-T content, gene arrangement and other features are more similar to putative ancestral mollusks than to other bivalves. Two supranumerary open reading frames are present in a large, otherwise unassigned, region, while the origin of replication could be located in a region upstream to the cox3 gene. Conclusions We show that S. velum mitogenome retains most of the ancestral conchiferan features, which is unusual among bivalve mollusks, and we discuss main peculiarities of this first example of an organellar genome coming from the subclass Opponobranchia. Mitochondrial genomes of Solemya (for bivalves) and Haliotis (for gastropods) seem to retain the original condition of mollusks, as most probably exemplified by Katharina.
Collapse
Affiliation(s)
- Federico Plazzi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Via Selmi, 3, Bologna 40126, Italy.
| | | | | |
Collapse
|
11
|
Meng X, Shen X, Zhao N, Tian M, Liang M, Hao J, Cheng H, Yan B, Dong Z, Zhu X. The complete mitochondrial genome of the clamMactra veneriformis(Bivalvia: Mactridae): Has a unique non-coding region, missingatp8and typicaltRNASer. ACTA ACUST UNITED AC 2013; 24:613-5. [DOI: 10.3109/19401736.2013.772152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
12
|
Meng X, Shen X, Zhao N, Tian M, Liang M, Hao J, Cheng H, Yan B, Dong Z, Zhu X. Mitogenomics reveals two subspecies inCoelomactra antiquata(Mollusca: Bivalvia). ACTA ACUST UNITED AC 2012; 24:102-4. [DOI: 10.3109/19401736.2012.726620] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|